From 34dc6e5a8125edb00f5bcf16ebe434aee8bfc3af Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Wed, 30 Oct 2024 11:17:32 +0000
Subject: [PATCH] adding params in config

---
 nf_core/pipeline-template/conf/test.config      | 6 ++++++
 nf_core/pipeline-template/conf/test_full.config | 6 ++++++
 nf_core/pipeline-template/nextflow.config       | 7 +++++++
 nf_core/pipeline-template/workflows/pipeline.nf | 8 +++++---
 4 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
index bea6f670d0..0c2f9392fc 100644
--- a/nf_core/pipeline-template/conf/test.config
+++ b/nf_core/pipeline-template/conf/test.config
@@ -31,4 +31,10 @@ params {
     // Genome references
     genome = 'R64-1-1'
     {%- endif %}
+
+    {% if downstream_samplesheets -%}
+    // Downstream samplesheets
+    generate_downstream_samplesheets = true
+    generate_pipeline_samplesheets   = 'rnaseq'
+    {%- endif %}
 }
diff --git a/nf_core/pipeline-template/conf/test_full.config b/nf_core/pipeline-template/conf/test_full.config
index aa3b70c1e5..e01c4a8bc6 100644
--- a/nf_core/pipeline-template/conf/test_full.config
+++ b/nf_core/pipeline-template/conf/test_full.config
@@ -26,4 +26,10 @@ params {
     // Fasta references
     fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
+
+    {% if downstream_samplesheets -%}
+    // Downstream samplesheets
+    generate_downstream_samplesheets = true
+    generate_pipeline_samplesheets   = 'rnaseq'
+    {%- endif %}
 }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0afaaa6785..05e82de55c 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -29,6 +29,13 @@ params {
     {% if citations %}multiqc_methods_description = null{% endif %}
     {%- endif %}
 
+    {% if downstream_samplesheet -%}
+    // Downstream samplesheet generation
+    generate_downstream_samplesheets      = false
+    generate_pipeline_samplesheets        = null
+    generate_pipeline_samplesheets_format = 'csv'
+    {%- endif %}
+
     // Boilerplate options
     outdir                       = null
     {% if modules %}publish_dir_mode             = 'copy'{% endif %}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index c268f6e5ba..fd7a29b904 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -47,9 +47,11 @@ workflow {{ short_name|upper }} {
     //
     // SUBWORKFLOW: Generate downstream samplesheets
     //
-    GENERATE_DOWNSTREAM_SAMPLESHEETS(
-        ch_samplesheet
-    )
+    if (params.generate_downstream_samplesheets) {
+        GENERATE_DOWNSTREAM_SAMPLESHEETS(
+            ch_samplesheet
+        )
+    }
     {% endif %}
 
     //